


In the End

by AuthenticSouthern



Category: Mass Effect
Genre: Action, Action & Romance, Alternate Ending, F/M, Indoctrination Theory, KaidanAlenko, Mass Effect 3, Paragon Commander Shepard, Post-Mass Effect 3, Soldier (Mass Effect)
Language: English
Status: Completed
Published: 2016-03-16
Updated: 2016-03-16
Packaged: 2018-05-27 00:34:15
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 3
Words: 4,271
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/6262270
Author URL: https://archiveofourown.org/users/AuthenticSouthern/pseuds/AuthenticSouthern
Summary: <blockquote class="userstuff">
              <p>Allison Shepard – savior of the Citadel, Hero of the Alliance – is presented with three neatly laid out choices by a weird god-like child.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> I wrote this after my very first disappointing run through of Mass Effect 3, before they even considered adding on more DLC to the end. I literally finished the game and then sat up and wrote this. It's not the best, but it's fueled by passion.
> 
> ~Starts right after the God-Child gives Shepard the three choices.~

Fighting Saren, the geth, the Reapers… It all came down to this? This God-Child?

Allison Shepard – savior of the Citadel, Hero of the Alliance – stared down at the child now, a glowing entity before her, as she bled out.

“That’s it? These are my choices?” She looked to the three options ahead of her, neatly laid out. Nothing in her life, in her messy career, had been so neat.

“Yes. These are the only logical choices.”

Allie stared to her left, the blue-ish controls. “The Illusive Man wanted to control the Reapers…”

“Yes, but he could not. I now give you that choice.”

“He was a mad man,” She spat, wincing. The thought of him made her angry – she was glad that bastard was dead. “There’s no way he was in the right! There’s no way, after all he did – after all the people he killed! – that he was right to control the Reapers.”

“He had the right idea, but he could not – “

“I know, I know. He couldn’t control the Reapers,” Shepard hung her head, physically and mentally exhausted. Her whole body ached, but she pushed aside the pain as best she could.

The God-Child nodded silently, waiting for her to make her choice.

“Synthesis,” Allie stated, staring in the middle.

The God-Child followed her gaze. “Yes. A logical conclusion.”

She turned her eyes now to the child; there was something off about him, but she couldn’t put her finger on it. Somewhere in the back of her mind, she knew this child – this thing – could not be trusted.

Shepard looked to her right at the red machinery. “Destruction.”

“You will destroy all synthetics,” The God-Child commented in its monotone voice. “Including the geth and your AI.”

“EDI,” She responded automatically, giving her comrade’s name. “Her name is EDI.”

It gave a single nod.

Allie sighed, feeling defeated for the first time in… Well, the first time ever, really. She had never felt defeated, never given up. In the darkest hour, she remained optimistic and hopeful. There had always been a way out before, always a light at the end of the tunnel. There had always been a friend to lend a helping hand.

“Kaidan,” She thought. “I wish you were here right now…”

But he wasn’t. He was back on Earth. Was he even still alive? The thought of what might have happened to him drove straight to her heart. She clenched her jaw, trying to will away the tears. Did he know she was on the Citadel?

And what of the rest of her team? Garrus, her most loyal and best friend. Tali… Liara… Were they all still fighting? Were they dead? From the window, she could see the battle raging in space and the fires that seemed to consume Earth.

“You must choose, Shepard,” The God-Child urged gently, interrupting her thoughts.

She tore her eyes from the ships outside to her three choices. No matter what, she would surely die. There was no denying that. At least… At least she had been able to say goodbye to her teammates. To Kaidan.

“You do not have much time left.”

The way Kaidan looked at her – they both knew this might be their last words.

“Shepard, your wounds are significant.”

He had kissed her, afraid it might be their last. She tried to put on a brave face for him, but he saw right through it. They both knew it was the end. How had it come to this? They were supposed to retire someplace warm and sunny…

“You must – “

“I know,” She replied harshly, her voice cracking with the emotional strain. “I must choose.”

She took a few hesitant, wobbling steps toward her choices, the God-Child followed easily, looking up at her with what she could only guess was expectancy. Shepard took a deep ragged breath, knowing what she must do.

“I have to destroy them.”

The God-Child blinked. “Shepard, that is not…”

“I’m damn well not going to try to control them,” She snapped at him, glaring down at the boy. “The Illusive Man was insane – I’m not going to follow in his footsteps. He turned against humanity – against the Alliance, the whole galaxy. I will not control them.”

She took a few limping steps towards the right; the God-Child followed.

“Shepard, synthesis will – “

“Synthesis will what? You know what synthesis will do? It will take away everything that makes this galaxy great – our uniqueness. The Protheans lost – Javik himself admitted it was because they were too unified, too similar. No, I value our differences.” The faces of her friends flashed through her mind – different races, yet unified! “We are all different, unique! There is a value in that that I cannot take away from them.”

She took a few more steps towards the right, gripping her pistol with determination now.

“But this will destroy your AI, the geth,” The God-Child sounded… different. Concerned? Worried?

Allison bowed her head, stopping her march for a moment. “It’s my only choice,” She said softly. EDI… It wasn’t an easy decision to make. Joker would surely never forgive her for it. But compared to the alternatives? She agreed with what Anderson had said – destroying the Reapers was their only option.

“You will not survive this choice,” He reminded her.

“I won’t survive any of them,” She said, lifting her head once more and limping towards her destination.

“This is not the most logical choice.” There it was again – a sound of concern in its voice.

“But it’s mine to make,” Shepard stood, feeling the adrenaline surge once more through her veins. She stood up straight, held her pistol high and moved forward.

“This is not – “

“Not what you wanted,” She said angrily. “You don’t want them destroyed. Every fifty thousand years, you destroy all organic life – and for what? So new organic life can grow only to be destroyed again later? That’s no future. There’s no hope in that. There’s no good in that – we deserve better.”

“Shepard – “

More determined than ever, Shepard advanced more quickly, limping less and less and her adrenaline surged. “This is for Thane!” She fired a shot. “This is for Mordin!” Another shot. “This is for Ashley! For Kaidan! For Palaven! Thessia!” Her heart was pounding, smoke was beginning to bellow out of the machine, but she wasn’t done. Each shot rang out with a name, a planet, a species that she treasured, until finally, a last passionate call: “For Earth!”

Instantly, the explosion surrounded her and she was consumed by the darkness.


	2. Chapter 2

**Summary for the Chapter:**

> Shepard awakes on Earth battered and bruised - had her encounter with the God-Child and his three choices all been a dream? She's ready to shake off her injuries and kick Reaper ass.

“Shepard! Damn it, Liara, she’s got to be around her somewhere! Shepard!”

“Kaidan, you need medical attention! You need to stop!”

“And, what, give up on Shepard? You know she’d never give up on us!”

“Yes, but reports are that no one survived…”

“I’ll believe it when I find her, but not before then. If anyone can survive that blast…”

“It’s Shepard, yes.”

“Liara! Look, over there! Shepard!”

The voices were foggy, distant, but she could make out their sources. She tried to speak, but her chest felt so tight – why did it feel so tight?

“Liara, help me!”

Kaidan, he was close. She could hear his footsteps, his rapid breath.

“Goddess!”

Liara. She was helping him; they were close.

“Garrus! I need you!” Kaidan’s voice was terribly desperate; his normal sense of calm collectiveness had disappeared.

“What is it?” An unmistakable Turian voice responded.

“Help me lift this! I think Shepard’s under here!”

What were they doing? She couldn’t open her eyes, they were stuck shut. She knew she was in trouble, but she almost didn’t care. She… She just destroyed the Reapers. She managed a smile, painful as it was, at the thought just as she felt a weight being lifted off her chest.

“Shepard!” The three voices called out in unison, mixtures of shock and joy at the sight of their Commander.

“I did it…” She managed to whisper.

“We need a doctor!” Kaidan hollered at the top of his lungs, then in the most gentle of tones, he tried to comfort his love: “Allison, it’s going to be okay. You’re going to be okay.” As he spoke, she could hear him choke up with emotion.

“Damn, Kaidan,” She thought, lacking the strength to put it into words. “I’ve never seen you worked up about anything.” 

Gently, he wiped the crusted blood from her eyes and she managed to peel them open just enough to see his face near hers.

“Kaidan…” She breathed his name as a sigh of relief, overjoyed to see his lovely face. That stupid haircut.

“Shh, don’t talk,” He insisted quietly and cradled her body gently to keep her head off the rubble beneath her.

A medic ran up, applied a dosage of Medi-Gel and she could feel the difference, though she was still in bad shape. “She needs to rest,” He insisted. “Take her to the clinic, over there.”

Kaidan nodded, scooping Shepard up into his arms with ease. “Kaidan, I was on the Citadel…”

“She’s delirious,” Liara commented, looking on with concern, holding Garrus’s arm tentatively.

“No, no,” Shepard coughed, shaking her head. “I was on the Citadel… Talked to the Crucible… Gave me three choices…”

Kaidan shushed her gently, “It’s okay, you’re going to be fine. Conserve your energy.” Then he nodded to the others, “Keep going – the men need you out there. I’ll stay with Shepard.”

“Keep us updated,” Garrus replied, looking down at Shepard with affection.

“Yes,” Liara added, “Please.”

They all looked to Shepard, the great hero, and all but Kaidan departed. The Major quickly made way to the clinic, “Shepard needs help!” He called, urging any and all medical staff he could find in the makeshift clinic. “This is Commander Shepard, damn it, and she cannot die!”

Allison was content being held, hearing Kaidan’s heart faintly beating through his armor, and resisted weakly when she was put down on the table.

“It’s okay,” Kaidan stroked her hair, now falling out of her trademark blonde bun. “I’m here, I’m not leaving you. Never again.”

“Kaidan, I was on the Citadel,” She insisted weakly again, now staring at him with determination.

“Allison,” His voice broke with emotion. “I saw it. You were knocked out by Harbringer’s beam. You didn’t leave Earth.”

“But… I saw it. Anderson, the Illusive Man…”

Kaidan frowned, “Anderson is here. I just saw him.”

Shepard’s eyes opened wide, she ignored the medical staff rushing now to attend her wounds. “What? No, no, I just saw him on the Citadel. The Illusive Man killed him, I watched him die.”

As if on cue, Kaidan’s Omni-Tool sounded: “Major Alenko. Any sign of Shepard?”

“Anderson?” Shepard’s eyes lit up at the sound of his voice. He was alive?

Kaidan met her eyes with an easy smile, “Yes Sir.”

“Damn glad,” The Admiral gruffly remarked, obviously concerned for her well-being. Gunfire sounded from his channel. “Keep her safe, Alenko. Anderson out.”

“I wasn’t on the Citadel…” Allison furrowed her brow, thinking.

“No,” Kaidan whispered, stroking the side of her face lightly.

“Anderson… He’s been here. He’s alive. I’m alive. The Illusive Man – “

“No reports of him, Allie.”

“The Crucible, I talked to it – a little child, a God,” Her voice broke. Was she insane? Had she lost her mind? It was so real, so painfully real. It couldn’t have been a figment of her imagination.

“Oily shadows…” The words of the Rachni Queen suddenly echoed in her head. Her dreams… The nightmares she had been having – she had seen oily shadows! The Queen spoke of the Rachni Wars when her people had been indoctrinated by the Reapers. Shepard had heard stories of what indoctrination was like: the voices, the visions, the confusion, the humming. What if…?

Suddenly, there were voices of panic nearby – the Reapers were attacking the makeshift clinic, their forces were here.

“I need to get up,” Shepard insisted, trying to sit up. “I need to fight!”

“Allison,” All his worry and pent up concern shone through in her name.

“No, Kaidan, I’m just dead weight if I can’t walk – I walk or I die. You can’t carry me and shoot straight at the same time! Damn it, get me on my feet!”

“Commander, your body is damaged enough. Pumping you with meds would get you on your feet, but you’d be doing more damage to it just by walking!” The doctor was hesitant.

“You heard the Commander,” Kaidan said wearily. “She’s too stubborn to listen to reason, trust me. Do what she says or she’ll do it without the meds.”

Shepard nodded defiantly and the doctor caved in. “You’re going to kill yourself,” He insisted.

“I’ll take some Reapers down with me, then,” Shepard responded, feeling instantly much better, surging with false energy.

An explosion from the south caught their attention and Allison stood next to Kaidan, grasping her pistol firmly. She ached, but the worst of her pain was muted.

“Here, Commander, you’ll need more than that,” A voice came from behind. She turned to see James holding an assault rifle and a grin. He had apparently not heard of her near death experience because there was no sorrow in his eyes, only joy and a hint of flirtatious lust.

“Thanks Vega,” Allison replied with a grin and caught the rifle as he tossed it.

“Ready to kick some ass, Kaidan?” James stood on the other side of Shepard, leaving her sandwiched in the middle of the two men.

Kaidan did not return Vega’s mischievous smile, “It’s about time you showed up, Lieutenant.” The Major was not overly fond of men who flirted shamelessly with their superiors, not to mention his girlfriend.

“Shut the Hell up, the both of you,” Shepard snapped. Kaidan couldn’t help but grin seeing her strength return. “They’re coming!”

Two Mauraders crashed through the large front window, easily picking off the unarmed med staff nearby. They bellowed as they saw Shepard’s familiar face and opened fire.

Shepard and crew took cover; James launched a grenade that took out one of the Mauraders. “Oh yeah!” He cried out, glancing to Shepard for approval. Kaidan snarled and thrust a deadly biotic attack at the other deformed Turian, launching the thing into a wall while Shepard neatly fired a few shots into its torso, finishing it off.

“We’ve got to get you somewhere safe!” Kaidan called above the battle sounds.

“Bullshit, Major! We’ve got to get to the Crucible!” Shepard cried, her throat painfully hoarse now. “We’ve got to destroy these things!”

“She has a good point,” Vega added, getting only a dirty look from Kaidan.

“Stop it, both of you! James! You go find Anderson!” Allison thrust a finger out towards the battle, signaling for him to get out of there.

“But – !”

“But nothing! Go!”

The giant of a man seemed half his size, bending to the will of one petite blond woman’s demands. “Just be careful out there, Lola,” He said with his usual grin, ignoring the Major flinching at the sound of the nickname.

“I’ll do what I can, Lieutenant,” She said firmly, adding in rank for her boyfriend’s sake. “Now go. You’ve got to save the Earth, Vega.”

He smirked, “Can’t do it without me.”

Shepard smiled, “Nope.”

“Later, Commander. Stay safe,” Then he nodded to Kaidan. “Major.”

“Lieutenant,” He replied. And he was off into the sea of soldiers and death.

“Kaidan, ready to do this?” Shepard crouched next to him, wanting to do so much more than bump elbows. Now was not a time for romance, she reminded herself.

“Ready as I’ll ever be. You sure about this?”

“Damn sure.”

###

They could see the beacon ahead, but now they crossed to it stealthily, hiding between the piles of rubble. Harbringer was still there, focused elsewhere at the moment. All attempts to reach the beam had so far failed miserably.

“Shepard?”

She looked to see Garrus amongst the rubble, tending to a wounded Turian soldier on the brink of death.

“What are you doing?” He seemed surprised to see her in action, though he shouldn’t, knowing her track record.

“Defying the odds,” Kaidan replied, looking at her with love in his eyes.

“You’re going for the Crucible again?”

“I’m going to try until I’m dead,” She said harshly, meaning every word. She would fight until her last breath, that was for damn sure.

“I’m coming with you,” He insisted.

“No, with the two of us we might be able to sneak in quietly. You need to stay here, help the wounded.” She gestured to the fallen Turian.

Garrus adjusted his mandibles, looking positively determined. “I’m coming with you. I can cover you, at the very least.” The wounded soldier gave a barely noticeable nod of approval. The mission must come first.

Allison smiled, knowing he’d come along one way or the other. “Fine, stay under cover – if we can – “

Her train of thought was interrupted as another squad of men surged down towards the beam, hoping that brute force and sheer number would be on their side. Harbringer immediately focused its beam onto the helpless troups. “Damn it,” Shepard muttered, but she knew this would provide an excellent distraction. Now there were no husks swarming them, they were being concentrated on the charging soldiers.

“Now’s our chance,” Garrus whispered. Kaidan nodded, looking to Shepard for the signal to move.

She nodded. It was now or never.

The trio snuck quietly to the beam – ducking, kneeling, and crawling all the way. It was hard for Allison to imagine that she hadn’t done this before already. Well, she had made it halfway, at least, but her memory still believed she had made it the whole way. The God-Child had seemed so real – had it all been false? Had it all been a fabrication of her mind?

###

Finally, they reached the beam and without hesitation, the three leapt into it.

For a moment, all was white.

White light, radiating everywhere.


	3. Chapter 3

**Summary for the Chapter:**

> Shepard finally reaches the Crucible - no God-Child, no three choices. It's time to end this once and for all, but Harbringer won't go down easily.

Shepard blinked and she was aboard the Citadel, the Crucible. It was not like it was before – no bodies littered the floor. There were no three choices, just the large room with the control panel like she had seen before.

She looked around, waiting for the God-Child, but nothing appeared.

“Kaidan? Garrus?” She asked hesitantly.

“Allison, we made it,” Kaidan breathed a sigh of relief. She wanted to slip her arms around him, embrace him tightly, but there was no time.

“This is… Not what I expected,” Garrus said, taking in the sight.

The three walked slowly towards the controls, guns drawn and eyes peeled. But there was… Nothing.

:SHEPARD:

A voice came from everywhere and nowhere at the same time, the same voice she had heard countless times before: a Reaper. Harbringer.

:SHEPARD:

She knew now where the voice was coming from – she could hear it inside her head, grating against her skull. She closed her eyes, grabbed at her hair.

“Allison, what’s wrong?” Kaidan turned to her quickly.

“Kaidan, it’s… inside my head. Harbringer. I can… hear it.”

“You’ve got to fight it, Shepard,” Garrus encouraged.

“That’s what happened before… I was indoctrinated, but I fought it.” It felt as if her skull now weighed a thousand pounds as the Reaper bore down on her, using all its strength on her free will. Her breathing was ragged now as she struggled to remain in control of her head. It had hoped to gain control over her before – this was its last chance.

“Keep fighting, Allison!” Kaidan urged.

“I’ll see what I can do with this,” Garrus said, jogging to the panel. He pulled up the screen and fiddled with it. “There! The arms are opening!” The arms of the Citadel began to open and they could hear excited radio chatter as the Crucible moved into place.

:SHEPARD. I AM IN CONTROL:

“No! You cannot control me!” She nearly collapsed to her knees, trying to force the Reaper out.

“Allison, I know you can do this,” Kaidan coached her with a gentle urging.

“The Crucible is in place!” Garrus reported, knowing the other two were far too preoccupied to notice themselves. “It’s not doing anything…”

:YOU CANNOT WIN:

“Kaidan! I can’t figure this out!” Garrus called. “The Crucible isn’t doing anything!”

“Allison needs me!”

“The galaxy needs you!”

:THIS HURTS YOU:

A wave of pain crossed her body and she convulsed, her legs buckling beneath her. Once more, Kaidan cradled her in his arms. “Whoa! Easy now,” He grabbed her, holding her firmly was the only thing he could think to do.

:ASSUMING DIRECT CONTROL:

“No!” Shepard cried out, focusing all her willpower to keep the damned thing out of her body. “You will not take me!”

“Kaidan!” Garrus called, frantically trying to operate the controls. “I need you!”

Shepard’s muscles seized as Harbringer gained control. She stood up, flexing her arms out and pushed Kaidan away roughly.

“Allison?”

Shepard retrieved her assault rifle from her back and pointed it at Kaidan.

“Allison, no!”

Garrus turned and in an instant pulled his sniper rifle, aiming at Shepard. “Harbringer has taken her over, Kaidan! She’s indoctrinated!”

:THIS HURTS YOU. YOU CANNOT RESIST:

Shepard’s finger lingered above the trigger, but Kaidan didn’t pull out his gun.

“Allison, please,” He said gently, emotion flooding his voice. “No, you have to fight this. I know you can fight this.”

:WE ARE YOUR DESTINY:

“I can’t… I can’t kill you,” He looked at her helplessly.

A red dot appeared Shepard’s head as Garrus watched her through his scope. “Kaidan…”

“Garrus! Stand down!” Kaidan yelled, his voice harsh.

Shepard’s body swayed, but the rifle remained pointed at Kaidan.

:YOUR DESTINY:

“I said STAND DOWN!”

Garrus let out a low, guttural growl, “I can’t do that, Kaidan.” Emotion swept over the Turian now, but unlike Kaidan, his thoughts were on the bigger picture.

:THIS HURTS YOU:

Shepard’s rifle quivered in her hand.

“GARRUS, STAND DOWN!”

“I CAN’T DO THAT, MAJOR!”

:WE ARE YOUR DESTINY. RESISTANCE IS FUTILE:

Allison’s hand holding the rifle began to shake wildly. Garrus gripped his own rifle tighter.

“No!” Shepard’s voice rang out, shaking as much as her arm. Her jaw clenched, her eyes were wild. With all her remaining strength, she fought the last of the Reaper influence lingering in her mind. “No!” She cried out again, her will prevailing slowly.

Kaidan looked on eagerly, hoping beyond hope that she would come through. If anyone could, it was Shepard.

“I… cannot…fail!” Her rifle dropped from her hand with a loud thud, her arms fell heavily to her side.

“Allison?”

“Stay back!” She cried to Kaidan, grimacing at him. She took a step towards the console, a painfully heavy step. “He’s… in my head! Stay back!”

She could feel the Reaper digging into her skull, picking at her brain, trying to force her body away from the control panel.

Now she heard the God-Child’s voice echoing in her mind: “Shepard, you cannot win. You cannot succeed. I gave you the choices and you chose wrong. You will only bring forth destruction now. You cannot resist.”

“No,” She muttered, slowly marching towards the console. This was her only choice, her only option. The Reapers, this God-Child hallucination, didn’t want her to reach that panel. She had passed it up before and was lead to her three choices. She knew now that it was false – the Reapers had been silently digging into her brain for months, years even!

“This will destroy all synthetic life. The geth that you saved – that you risked your life for.”

“I don’t trust… anything you say…” It was a struggle to speak.

Kaidan and Garrus watched silently and helplessly, unsure of what to do now.

“EDI will surely perish. All technology will be gone.”

“You will not… control me…” She was nearly there, unsure of what she would do when she got there.

“The Mass Relays will be destroyed. Your fleets here, they will be stranded in this system.”

“You’re… pathetic,” Shepard spat. “You’re scared…”

:WE DO NOT FEAR YOU:

The Reaper’s voice once again boomed in her head and her vision was suddenly clouded by slinking black shadows.

“Oh yeah?” Shepard grimaced, nearly within reach now… “You’re desperate, grasping at straws… Trying to save your asses…”

Suddenly, Garrus’s radio broke into noise: -The Reapers are turning from the fleets! They’re… They’re moving towards the Crucible, the Citadel!-

“No!” Garrus cried into his Omni-Tool frantically.

-All troops, protect the Crucible at all costs!-

The sounds of gunfire seemed to get louder as the battled raged closer and closer to the Crucible.

Shepard finally reached the control panel and she slammed her palms down on the thing, exhausted, but not done. The pain was almost unbearable, she was surprised her ears weren’t bleeding from the sheer pressure of the force bearing down on her now.

“Victory…” Shepard’s voice was weak, her fingers caressed the keys firmly and slowly.

“Allison,” Kaidan said breathlessly, reaching out for her in seemingly slow motion now.

:YOUR FORM IS WEAK. WE ARE YOUR DESTINY:

“Shepard!” Garrus cried out to her, raising his rifle again at her just in case. 

“… at all… “ It was as if her fingers knew just where to go. She needed no direction.

:YOU CANNOT WIN. YOU WILL FAIL:

“ … costs.” The last keystroke sent out a beam of white light and surrounded Shepard, blinding her comrades. She felt her body being lifted up into the air, like the beacon on Eden Prime, and all sound faded away. Garrus let out a cry, sounding more like a bellowing roar of frustration. Kaidan’s desperate cries were drowned out, the sounds of the raging battle – gone.

Silence.

###


End file.
